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Well, you can assume that the Legendaries you face won't be EV Trained, but that isn't always the case... Since most battles are usually in Normal Rules(Meaning LV 50 is the LV Cap), there is no way for you to tell what LV the Legendary Pokemon actually is. The only way you can find put a level of a Pokemon is with the No Restrictions cap in the game, which does what it says basically... While there are people who don't even know what EVs are and think Legendaries are all too powerful, it's not safe enough to say that the have no EVs, because sometimes they do. Also, when you said that you raised your Mewtwo to LV 100, that LVing up gains EVs alone, maybe not max EVs in a stat, but EVs all around.

So the ultimate answer is no, never expect the best, but always the worst.